Contacts of the strand formed by residues 67 - 72 (chain A) in PDB entry 5K26


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ARG 67 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  VAL*     3.7    25.2    -      -       +      +
     46A  TRP      3.4     4.0    -      -       -      -
     47A  THR*     4.2    15.4    +      -       +      +
     65A  GLY      3.4     7.1    +      -       -      +
     66A  ASP*     1.3    72.8    -      -       -      +
     68A  VAL*     1.3    60.2    +      -       -      +
     87A  GLN      4.1     2.8    -      -       -      +
     88A  VAL*     3.7    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  VAL*     3.3     3.8    -      -       -      -
     46A  TRP*     2.8    42.0    +      -       -      +
     48A  ALA      4.6     1.6    -      -       -      +
     60A  LEU*     4.4     3.1    -      -       +      -
     62A  LEU*     3.8    17.5    -      -       +      -
     66A  ASP*     3.9    12.6    -      -       +      +
     67A  ARG*     1.3    75.9    -      -       -      +
     69A  GLU*     1.3    70.9    +      -       -      +
     70A  VAL*     3.4     5.3    +      -       +      +
     86A  GLY*     4.2     4.0    -      -       -      -
     87A  GLN      3.7     4.5    -      -       -      +
     88A  VAL*     3.6    21.5    -      -       +      -
     95A  PHE*     3.8    31.2    -      -       +      -
    100A  VAL*     4.3    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     4.5     6.3    -      -       -      +
     43A  ASN*     2.8    55.5    +      -       +      +
     44A  PRO      3.6     3.6    -      -       -      -
     45A  VAL*     4.3    11.6    -      -       +      +
     67A  ARG      4.2     0.8    +      -       -      -
     68A  VAL*     1.3    69.2    -      -       -      +
     70A  VAL*     1.3    59.6    +      -       -      +
     71A  LEU*     3.5    10.8    +      -       +      +
     86A  GLY*     3.1     4.3    -      -       -      -
     87A  GLN*     2.8    57.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ASN*     3.4    18.2    -      -       -      +
     44A  PRO*     2.9    23.1    +      -       +      +
     46A  TRP*     3.5    33.0    -      -       +      +
     68A  VAL*     3.8     7.4    -      -       +      +
     69A  GLU*     1.3    72.1    -      -       -      +
     71A  LEU*     1.3    63.2    +      -       -      +
     72A  SER*     4.0     7.4    -      -       -      +
     73A  ARG*     3.7    33.7    -      -       +      -
     84A  TRP*     4.2     8.7    -      -       +      -
     85A  ALA      3.7     9.2    -      -       -      +
     86A  GLY*     4.4     0.2    -      -       -      -
     95A  PHE*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ASN*     3.6    33.0    -      -       -      +
     69A  GLU*     4.1    21.1    -      -       +      +
     70A  VAL*     1.3    75.0    -      -       -      +
     72A  SER*     1.3    59.7    +      -       -      +
     85A  ALA*     2.8    19.9    +      -       +      +
     86A  GLY*     4.4     4.9    -      -       -      +
     87A  GLN*     4.4    10.8    -      -       -      +
     92A  VAL*     4.0    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  VAL*     3.6     1.5    -      -       -      -
     71A  LEU*     1.3    82.0    -      -       -      +
     73A  ARG*     1.3    64.3    +      -       -      +
     74A  ASP*     3.1    26.7    +      -       -      +
     84A  TRP*     3.5     6.1    -      -       -      +
     85A  ALA*     2.9    38.2    +      -       -      +
    201A  MES      5.2     3.1    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il